'''
Created on Oct 10, 2009

@author: mkiyer
'''

from veggie.app.alignment.novoalign import Novoalign
import sys

if __name__ == '__main__':
    fastq_file = sys.argv[1]
    # create the app controller    
    novoalign_app = Novoalign()
    novoalign_app.run([fastq_file], 'solexa-quals', genome="hg18")
    